万字长文介绍R package “vegan”——入门学习与重复文献数据

vegan介绍与入门

vegan是一个用于群落生态学（community ecology）分析的包，可以进行排序、多样性和差异性分析（ordination, diversity and dissimilarity）。

vegan包含了多样性分析、排序方法和差异性分析的工具。

示例一：unconstrained analysis（非约束排序）

### example1: unconstrained analysis
## NMDS
library(vegan)

data(varespec)
data("varechem")

ord = metaMDS(varespec)
plot(ord, type = "t")

# fit environmental variables
ef = envfit(ord, varechem)
ef
plot(ef, p.max = 0.05)

> ef

***VECTORS

            NMDS1    NMDS2     r2 Pr(>r)    
N        -0.05729 -0.99836 0.2536  0.035 *  
P         0.61969  0.78484 0.1938  0.108    
K         0.76642  0.64234 0.1809  0.109    
Ca        0.68517  0.72838 0.4119  0.004 ** 
Mg        0.63250  0.77456 0.4270  0.002 ** 
S         0.19135  0.98152 0.1752  0.119    
Al       -0.87162  0.49019 0.5269  0.001 ***
Fe       -0.93604  0.35190 0.4450  0.002 ** 
Mn        0.79872 -0.60171 0.5231  0.001 ***
Zn        0.61754  0.78654 0.1879  0.109    
Mo       -0.90308  0.42948 0.0609  0.526    
Baresoil  0.92491 -0.38019 0.2508  0.045 *  
Humdepth  0.93284 -0.36029 0.5200  0.001 ***
pH       -0.64800  0.76164 0.2308  0.061 .  
---
Signif. codes:  
0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Permutation: free
Number of permutations: 999

示例二：constrainted analysis（约束排序）

### example2: constrained ordination (RDA)
## the example uses formula interface to define the modle

library(vegan)

data("dune")
data("dune.env")

# no constraints: PCA
mod0 = rda(dune ~ 1, dune.env)
mod0
plot(mod0)

# all environmental variables: Full model
mod1 = rda(dune ~ ., dune.env)
mod1
plot(mod1